fslr: Wrapper Functions for FSL ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Wrapper functions that interface with 'FSL' (http:// fsl.fmrib.ox.ac.uk/fsl/fslwiki/), a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'FSL' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'FSL' command and returns an R object of class 'nifti' if desired.

Author
John Muschelli <muschellij2@gmail.com>
Date of publication
2016-09-28 19:35:02
Maintainer
John Muschelli <muschellij2@gmail.com>
License
GPL-3
Version
2.0

View on CRAN

Man pages

aux_file-methods
Extract Image aux.file attribute
bitpix-methods
Extract Image bitpix attribute
cal_max-methods
Extract Image cal.max attribute
cal_min-methods
Extract Image cal.min attribute
check_file
Wrapper for getForms with filename
checkout
Determine of Q and S forms are consistent
data_type-methods
Extract Image data_type attribute
datatype-methods
Extract Image datatype attribute
descrip-methods
Extract Image descrip attribute
dim_-methods
Extract Image dim_ attribute
download_fsl
Download FSL
dtifit
DTI Fitting Procedure from FSL
eddy_correct
Eddy Current Correction
fast
FSL FAST
fast.help
FAST help
flirt
Register using FLIRT
flirt_apply
Apply Warp from FLIRT
flirt.help
FLIRT help
fnirt
Register using FNIRT
fnirt.help
FNIRT help
fnirt_with_affine
Register using FNIRT, but doing Affine Registration as well
fnirt_with_affine_apply
Applies FLIRT then FNIRT transformations
fslabs
Absolute Value Image using FSL
fslabs.help
fslabs Help
fslacos
Arc Cosine Transform Image using FSL
fslacos.help
fslacos Help
fsladd
Add Images using FSL
fsladd.help
fsladd Help
fsl_anat
FSL Anatomical Processing Script
fsl_anat.help
fsl_anat help
fsl_applywarp
Apply Warp from FNIRT
fsl_applywarp.help
FSL applywarp help
fslasin
Arc Sine Transform Image using FSL
fslasin.help
fslasin Help
fslatan
Arc Tangent Transform Image using FSL
fslatan.help
fslatan Help
fsl_atlas_dir
Get FSL's Standard Data Directory
fslbet
Use FSL's Brain Extraction Tool (BET)
fslbet.help
Help for FSL BET
fsl_biascorrect
FSL Bias Correct
fslbin
Binarize Image using FSL
fslbin.help
fslbin Help
fslbinv
Binarized Inverse Image using FSL
fslbinv.help
fslbinv Help
fslchfiletype
FSL Change file type
fslchfiletype.help
fslchfiletype help
fslcmd
FSL Command Wrapper
fslcog
Image Center of Gravity (FSL)
fslcos
Cosine Transform Image using FSL
fslcos.help
fslcos Help
fslcpgeom
FSL Copy Geometry
fslcpgeom.help
fslcpgeom help
fsl_data_dir
Get FSL's Data Directory
fsldilate
Dilate image using FSL
fsldir
Get FSL's Directory
fsldiv
Divide Images using FSL
fsldiv.help
fsldiv Help
fsledge
Edge Strength Image using FSL
fsledge.help
fsledge Help
fslentropy
Image Mean Entropy
fslerode
Erode image using FSL
fslerode.help
fslerode Help
fslexp
Exponentiate Image using FSL
fslexp.help
fslexp Help
fslfill
Fill image holes
fslfill2
Fill image holes with dilation then erosion
fslfill.help
fslfill Help
fslhd
Get NIfTI header using FSL
fslhd.help
FSLhd help
fslhd.parse
Parse FSL Header
fslhelp
Wrapper for getting fsl help
fslindex
Index Image using FSL
fslindex.help
fslindex Help
fsllog
Log Transform Image using FSL
fsllog.help
fsllog Help
fslmask
Mask image using FSL
fslmask.help
fslmask Help
fslmaths
FSL Maths
fslmaths.help
FSL Maths Help
fslmean
Image Mean
fslmerge
Merge images using FSL
fslmerge.help
FSLMerge help
fslmul
Multiply Images using FSL
fslmul.help
fslmul Help
fslnan
Replace NaNs in Image using FSL
fslnan.help
fslnan Help
fslnanm
Mask NaNs in Image using FSL
fslnanm.help
fslnanm Help
fslorient
FSL Orient
fslorienter
Wrapper for FSL Get Orientation
fslorient.help
fslorient help
fslorient_wrap
FSL Orientation Wrappers
fslrand
Add Random Uniform Noise Image using FSL
fslrand.help
fslrand Help
fslrandn
Add Random Standard Guassian Noise Image using FSL
fslrandn.help
fslrandn Help
fslrange
Get range of an image
fslrecip
Reciprocal Image using FSL
fslrecip.help
fslrecip Help
fslrem
Modulus Remainder of 2 Images using FSL
fslrem.help
fslrem Help
fslreorient2std
FSL Orient to MNI
fslreorient2std.help
fslreorient2std help
fslroi
FSL ROI
fslsd
Image Standard Deviation
fslsin
Sine Transform Image using FSL
fslsin.help
fslsin Help
fsl_slicetimer
FSL Slice Timing Correction
fslsmooth
Gaussian smooth image using FSL
fslsmooth.help
fslsmooth Help
fslsplit
Split images using FSL
fslsplit.help
FSL Split help
fslsqr
Square Image using FSL
fslsqr.help
fslsqr Help
fslsqrt
Square Root Image using FSL
fslsqrt.help
fslsqrt Help
fslstats
FSL Stats
fslstats.help
FSL Stats Help
fsl_std_dir
Get FSL's Standard Data Directory
fslsub
Subtract Images using FSL
fslsub2
Subsample image by factor of 2
fslsub2.help
fslsub2 Help
fslsub.help
fslsub Help
fslsum
FSL Sum
fslswapdim
FSL Swap Dimensions
fslswapdim.help
fslswapdim help
fsltan
Tangent Transform Image using FSL
fsltan.help
fsltan Help
fslthresh
Threshold an image
fslthresh.help
fslthresh Help
fslval
Get value from FSL header
fslval.help
fslval help
fsl_version
Find FSL Version
fslview
Open image in FSLView
fslview.help
FSLView help
fslvol
FSL Volume in mL (or cubic centimeters)
fslvolume
Image Volume
getForms
Get Q and S Forms of orientation matrix
get.fsl
Create command declaring FSLDIR
get.fsloutput
Determine FSL output type
get.imgext
Determine extension of image based on FSLOUTPUTTYPE
have.fsl
Logical check if FSL is accessible
intent_code-methods
Extract Image intent_code attribute
intent_name-methods
Extract Image intent_name attribute
intent_p1-methods
Extract Image intent_p1 attribute
intent_p2-methods
Extract Image intent_p2 attribute
intent_p3-methods
Extract Image intent_p3 attribute
magic-methods
Extract Image magic attribute
mcflirt
FSL Motion Correction
mcflirt.help
MCFLIRT help
melodic
Run MELODIC ICA
melodic.help
MELODIC help
mni_fname
Construct MNI Filename
mni_img
Read MNI Filename
orientation-methods
Extract NIfTI 3D Image Orientation
pixdim-methods
Extract Image pixdim attribute
probtrackx
Probabilistic diffusion tractography with multiple fibre...
qform_code-methods
Extract Image qform_code attribute
run_first_all
Run FIRST All
run_first_all.help
Run FIRST All Help
scl_inter-methods
Extract Image scl_inter attribute
scl_slope-methods
Extract Image scl_slope attribute
sform_code-methods
Extract Image sform_code attribute
sizeof_hdr-methods
Extract Image sizeof_hdr attribute
slice_code-methods
Extract Image slice_code attribute
slice_duration-methods
Extract Image slice_duration attribute
slice_end-methods
Extract Image slice_end attribute
slice_start-methods
Extract Image slice_start attribute
susan
FSL SUSAN noise reduction
susan.help
FSL SUSAN Help
toffset-methods
Extract Image toffset attribute
vox_offset-methods
Extract Image vox_offset attribute
xfibres
Bayesian Estimation of Diffusion Parameters Obtained using...

Files in this package

fslr
fslr/inst
fslr/inst/CITATION
fslr/inst/doc
fslr/inst/doc/dti_data.Rmd
fslr/inst/doc/dti_data.R
fslr/inst/doc/fslr.R
fslr/inst/doc/fslr.html
fslr/inst/doc/dti_data.html
fslr/inst/doc/fslr.Rmd
fslr/NAMESPACE
fslr/R
fslr/R/intent_code.R
fslr/R/fslvol.R
fslr/R/fslrecip.R
fslr/R/scl_inter.R
fslr/R/fslnanm.R
fslr/R/fslexp.R
fslr/R/fslvolume.R
fslr/R/fslcpgeom.R
fslr/R/probtrackx.R
fslr/R/fslbin.help.R
fslr/R/fslsin.help.R
fslr/R/fsledge.R
fslr/R/applywarp.R
fslr/R/fslsub2.help.R
fslr/R/mcflirt.R
fslr/R/fsledge.help.R
fslr/R/fslchfiletype.R
fslr/R/fslmask.help.R
fslr/R/fsl_anat.R
fslr/R/fslatan.R
fslr/R/fslrandn.help.R
fslr/R/fslacos.R
fslr/R/susan.R
fslr/R/fslnan.R
fslr/R/fslsqrt.R
fslr/R/fnirt.R
fslr/R/fslindex.R
fslr/R/mni_fname.R
fslr/R/fslmean.R
fslr/R/fslasin.help.R
fslr/R/fslsub.R
fslr/R/fsldiv.R
fslr/R/sizeof_hdr.R
fslr/R/fsldiv.help.R
fslr/R/bitpix.R
fslr/R/fslrand.help.R
fslr/R/aux_file.R
fslr/R/fslrem.help.R
fslr/R/magic.R
fslr/R/datatype.R
fslr/R/fslfill2.R
fslr/R/fslhd.R
fslr/R/fsladd.R
fslr/R/fslentropy.R
fslr/R/import_methods.R
fslr/R/fslatan.help.R
fslr/R/fslrandn.R
fslr/R/fslcos.help.R
fslr/R/fslrand.R
fslr/R/fslsmooth.help.R
fslr/R/fsltan.R
fslr/R/intent_p3.R
fslr/R/cal_min.R
fslr/R/fslthresh.help.R
fslr/R/fslsd.R
fslr/R/slice_duration.R
fslr/R/intent_p1.R
fslr/R/dim_.R
fslr/R/sform_code.R
fslr/R/fslerode.help.R
fslr/R/fslabs.R
fslr/R/fsl_data_dir.R
fslr/R/fslsub.help.R
fslr/R/slice_end.R
fslr/R/fslmul.help.R
fslr/R/fsllog.R
fslr/R/xfibres.R
fslr/R/fslrem.R
fslr/R/slice_start.R
fslr/R/intent_name.R
fslr/R/eddy_correct.R
fslr/R/fslsum.R
fslr/R/data_type.R
fslr/R/fsltan.help.R
fslr/R/fslsplit.R
fslr/R/fslsqrt.help.R
fslr/R/fsl_slicetimer.R
fslr/R/fslbinv.help.R
fslr/R/fslsqr.R
fslr/R/fslacos.help.R
fslr/R/fslsqr.help.R
fslr/R/fslgetorient.R
fslr/R/scl_slope.R
fslr/R/vox_offset.R
fslr/R/fslsin.R
fslr/R/fslmul.R
fslr/R/qform.R
fslr/R/slice_code.R
fslr/R/run_first_all.R
fslr/R/fsl_version.R
fslr/R/fslcos.R
fslr/R/sform.R
fslr/R/fslindex.help.R
fslr/R/fslexp.help.R
fslr/R/fslbinv.R
fslr/R/toffset.R
fslr/R/pixdim.R
fslr/R/fslrecip.help.R
fslr/R/flirt_apply.R
fslr/R/fslfill.help.R
fslr/R/fslnanm.help.R
fslr/R/fsllog.help.R
fslr/R/fslasin.R
fslr/R/fslroi.R
fslr/R/fast.R
fslr/R/dtifit.R
fslr/R/fsladd.help.R
fslr/R/intent_p2.R
fslr/R/fslabs.help.R
fslr/R/cal_max.R
fslr/R/download_fsl.R
fslr/R/qform_code.R
fslr/R/descrip.R
fslr/R/fsldilate.R
fslr/R/fslnan.help.R
fslr/vignettes
fslr/vignettes/dti_data.Rmd
fslr/vignettes/fslr.Rmd
fslr/MD5
fslr/build
fslr/build/vignette.rds
fslr/DESCRIPTION
fslr/man
fslr/man/fslstats.help.Rd
fslr/man/get.imgext.Rd
fslr/man/vox_offset-methods.Rd
fslr/man/fsl_anat.Rd
fslr/man/melodic.Rd
fslr/man/fslbet.Rd
fslr/man/fslrandn.help.Rd
fslr/man/dtifit.Rd
fslr/man/melodic.help.Rd
fslr/man/fslrem.Rd
fslr/man/fslrecip.help.Rd
fslr/man/fslerode.Rd
fslr/man/intent_code-methods.Rd
fslr/man/fsl_data_dir.Rd
fslr/man/fslfill.help.Rd
fslr/man/fslroi.Rd
fslr/man/fslatan.Rd
fslr/man/cal_min-methods.Rd
fslr/man/fsl_applywarp.help.Rd
fslr/man/fslreorient2std.help.Rd
fslr/man/aux_file-methods.Rd
fslr/man/have.fsl.Rd
fslr/man/sform_code-methods.Rd
fslr/man/fslsin.Rd
fslr/man/fslsd.Rd
fslr/man/fslbet.help.Rd
fslr/man/fslorient.help.Rd
fslr/man/fslcpgeom.help.Rd
fslr/man/fslbin.help.Rd
fslr/man/get.fsl.Rd
fslr/man/fslindex.help.Rd
fslr/man/fsldilate.Rd
fslr/man/dim_-methods.Rd
fslr/man/download_fsl.Rd
fslr/man/fslmaths.Rd
fslr/man/susan.Rd
fslr/man/fsladd.Rd
fslr/man/fslcos.Rd
fslr/man/fslrecip.Rd
fslr/man/fsl_anat.help.Rd
fslr/man/fslasin.help.Rd
fslr/man/fslacos.help.Rd
fslr/man/fslerode.help.Rd
fslr/man/run_first_all.help.Rd
fslr/man/fslsub2.help.Rd
fslr/man/fsllog.Rd
fslr/man/fslsmooth.help.Rd
fslr/man/fslrand.help.Rd
fslr/man/fslhd.help.Rd
fslr/man/eddy_correct.Rd
fslr/man/fslabs.Rd
fslr/man/fslsplit.Rd
fslr/man/mni_img.Rd
fslr/man/fslnanm.Rd
fslr/man/fslsmooth.Rd
fslr/man/fslsplit.help.Rd
fslr/man/fslmask.Rd
fslr/man/fslcos.help.Rd
fslr/man/fslexp.help.Rd
fslr/man/run_first_all.Rd
fslr/man/fslsqrt.help.Rd
fslr/man/fslsin.help.Rd
fslr/man/fslbinv.help.Rd
fslr/man/descrip-methods.Rd
fslr/man/getForms.Rd
fslr/man/flirt_apply.Rd
fslr/man/fslbin.Rd
fslr/man/fslsub2.Rd
fslr/man/fslorienter.Rd
fslr/man/fslexp.Rd
fslr/man/sizeof_hdr-methods.Rd
fslr/man/fsllog.help.Rd
fslr/man/mcflirt.help.Rd
fslr/man/fsladd.help.Rd
fslr/man/fslatan.help.Rd
fslr/man/mni_fname.Rd
fslr/man/flirt.Rd
fslr/man/fslsum.Rd
fslr/man/datatype-methods.Rd
fslr/man/scl_slope-methods.Rd
fslr/man/qform_code-methods.Rd
fslr/man/fslstats.Rd
fslr/man/fslhelp.Rd
fslr/man/slice_code-methods.Rd
fslr/man/fslbinv.Rd
fslr/man/fslswapdim.help.Rd
fslr/man/slice_end-methods.Rd
fslr/man/fslcog.Rd
fslr/man/fast.Rd
fslr/man/fnirt.help.Rd
fslr/man/fsltan.Rd
fslr/man/fslrandn.Rd
fslr/man/fslview.Rd
fslr/man/intent_name-methods.Rd
fslr/man/fslrand.Rd
fslr/man/fsl_biascorrect.Rd
fslr/man/fslhd.parse.Rd
fslr/man/fslindex.Rd
fslr/man/fslval.help.Rd
fslr/man/fsl_version.Rd
fslr/man/fslsqr.help.Rd
fslr/man/orientation-methods.Rd
fslr/man/fslnan.Rd
fslr/man/fslrem.help.Rd
fslr/man/fslmaths.help.Rd
fslr/man/get.fsloutput.Rd
fslr/man/fsldiv.help.Rd
fslr/man/fslcpgeom.Rd
fslr/man/fsl_applywarp.Rd
fslr/man/fslabs.help.Rd
fslr/man/fsldiv.Rd
fslr/man/fslmerge.Rd
fslr/man/data_type-methods.Rd
fslr/man/checkout.Rd
fslr/man/fslthresh.help.Rd
fslr/man/fast.help.Rd
fslr/man/fslvolume.Rd
fslr/man/fsl_slicetimer.Rd
fslr/man/fnirt.Rd
fslr/man/magic-methods.Rd
fslr/man/fslacos.Rd
fslr/man/fnirt_with_affine.Rd
fslr/man/cal_max-methods.Rd
fslr/man/fslhd.Rd
fslr/man/fslview.help.Rd
fslr/man/fsl_std_dir.Rd
fslr/man/fslfill.Rd
fslr/man/fslcmd.Rd
fslr/man/fslnanm.help.Rd
fslr/man/fslnan.help.Rd
fslr/man/fslsqr.Rd
fslr/man/flirt.help.Rd
fslr/man/fslmerge.help.Rd
fslr/man/fsltan.help.Rd
fslr/man/fslentropy.Rd
fslr/man/fslfill2.Rd
fslr/man/fslmul.help.Rd
fslr/man/fnirt_with_affine_apply.Rd
fslr/man/fslval.Rd
fslr/man/fslsqrt.Rd
fslr/man/probtrackx.Rd
fslr/man/fsledge.help.Rd
fslr/man/fslmul.Rd
fslr/man/fslorient_wrap.Rd
fslr/man/fsldir.Rd
fslr/man/fslsub.Rd
fslr/man/fslchfiletype.Rd
fslr/man/fslsub.help.Rd
fslr/man/fslmask.help.Rd
fslr/man/slice_duration-methods.Rd
fslr/man/fsledge.Rd
fslr/man/bitpix-methods.Rd
fslr/man/intent_p2-methods.Rd
fslr/man/scl_inter-methods.Rd
fslr/man/fsl_atlas_dir.Rd
fslr/man/fslchfiletype.help.Rd
fslr/man/toffset-methods.Rd
fslr/man/pixdim-methods.Rd
fslr/man/fslreorient2std.Rd
fslr/man/intent_p3-methods.Rd
fslr/man/fslswapdim.Rd
fslr/man/xfibres.Rd
fslr/man/susan.help.Rd
fslr/man/check_file.Rd
fslr/man/fslmean.Rd
fslr/man/fslvol.Rd
fslr/man/fslasin.Rd
fslr/man/intent_p1-methods.Rd
fslr/man/fslorient.Rd
fslr/man/fslthresh.Rd
fslr/man/mcflirt.Rd
fslr/man/slice_start-methods.Rd
fslr/man/fslrange.Rd